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https://github.com/mrolm/drep
Rapid comparison and dereplication of genomes
https://github.com/mrolm/drep
assembly bioinformatics metagenomics microbial-genomes microbiology
Last synced: 4 days ago
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Rapid comparison and dereplication of genomes
- Host: GitHub
- URL: https://github.com/mrolm/drep
- Owner: MrOlm
- Created: 2016-09-27T23:55:43.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-12-19T15:40:35.000Z (about 1 month ago)
- Last Synced: 2025-01-18T02:02:38.187Z (4 days ago)
- Topics: assembly, bioinformatics, metagenomics, microbial-genomes, microbiology
- Language: Python
- Homepage:
- Size: 16.5 MB
- Stars: 272
- Watchers: 8
- Forks: 38
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
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README
# dRep
[](https://pepy.tech/project/drep)
[](https://pepy.tech/project/drep)
dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.
Manual, installation instructions, and API are at available at
[ReadTheDocs](https://drep.readthedocs.io/en/latest/)
Publication is available at
[ISMEJ](https://doi.org/10.1038/ismej.2017.126)
Open source pre-print publication is available at
[bioRxiv](https://doi.org/10.1101/108142)
## Installation with pip
```
$ pip install drep
```
## Quick start
### Genome comparison:
```
$ dRep compare output_directory -g path/to/genomes/*.fasta
```
### Genome de-replication:
```
$ dRep dereplicate output_directory -g path/to/genomes/*.fasta
```
### Make sure dependencies are properly installed:
```
$ dRep check_dependencies
```
## Dependencies
### Near Essential
* [Mash](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x>) - Makes primary clusters (v1.1.1 confirmed works)
* [MUMmer](http://mummer.sourceforge.net/) - Performs default ANIm comparison method (v3.23 confirmed works)
### Optional
* [fastANI](https://github.com/ParBLiSS/FastANI) - A fast secondary clustering algorithm
* [CheckM](http://ecogenomics.github.io/CheckM/)_ - Determines contamination and completeness of genomes (v1.0.7 confirmed works)
* [gANI (aka ANIcalculator)](https://ani.jgi-psf.org/html/download.php?) - Performs gANI comparison method (v1.0 confirmed works)
* [Prodigal](http://prodigal.ornl.gov/) - Used be both checkM and gANI (v2.6.3 confirmed works)
* [NSimScan](https://pubmed.ncbi.nlm.nih.gov/27153714/) - Only needed for goANI algorithm (open source version of gANI)